The Genetic Architecture of Gliomagenesis–Genetic Risk Variants Linked to Specific Molecular Subtypes
Abstract
:1. Introduction
2. Results
2.1. Descriptive Characteristics of Datasets
2.2. Gliomagenesis Models
2.2.1. Genetic Variants Associated with all Glioma
2.2.2. Genetic Variants Associated with IDH-wt Glioma
2.2.3. Genetic Variants Associated with IDH-Mutant Glioma
2.3. Genetic Effects on the Gene Expression Levels
3. Discussion
3.1. All Glioma Risk Genes
3.2. IDH-wildtype Glioma Risk Variants
3.3. IDH-Mutant Glioma Risk Variants
3.4. Limitations
4. Materials and Methods
4.1. Swedish GICC Study Population
4.2. Genotyping and Imputation in Swedish GICC Study
4.3. Immunohistochemistry in Swedish GICC Study
4.4. Fluorescent In Situ Hybridization (FISH) in Swedish GICC Study
4.5. Statistical Analysis
4.6. Expression Quantitative Trait Locus Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Study | Current Study | Labreche et al., 2018 [9] | Eckel-Passow et al., 2019 [10] | |||||
---|---|---|---|---|---|---|---|---|
TCGA | French GWAS | French Sequencing | Subtotal Subjects | Mayo Clinic | UCSF | Subtotal Subjects | ||
Controls, N | 876 | 2648 | 1190 | 5527 | 9365 | 443 | 231 | 674 |
Male, N (%) | 516 (58.9) | NA | NA | NA | NA | 250 (56.4) | 121 (54.4) | 371 (55.0) |
Age, median (range) | 59 (21–82) | NA | NA | NA | NA | 56 (22–84) | 54 (18–89) | NA (18–89) |
Cases, N | 330 | 521 | 1423 | 704 | 2648 | 1273 | 852 | 2125 |
Male, N (%) | 135 (40.9) | NA | NA | NA | NA | 748 (58.8) | 495 (48.1) | 1243 (58.5) |
Age, median (range) | 59 (22–81) | NA | NA | NA | NA | 48 (18–84) | 51 (19–87) | NA (18–87) |
GBM, N (%) | 207 (62.7) | 183 (35.12) | 430 (30.2) | 181 (25.7) | 795 (30.0) | 481 (37.8) | 410 (48.1) | 891 (41.9) |
Molecular subtypes | ||||||||
IDH-wildtype, N | 258 | 55 | 450 | 277 | 782 | 165 | 335 | 500 |
IDH-mutant and 1p/19q intact, N | 29 | 104 | 215 | 209 | 528 | 141 | 133 | 274 |
IDH-mutant and 1p/19q co-deleted, N | 19 | 65 | 85 | 199 | 349 | 96 | 92 | 188 |
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Wu, W.Y.-Y.; Johansson, G.; Wibom, C.; Brännström, T.; Malmström, A.; Henriksson, R.; Golovleva, I.; Bondy, M.L.; Andersson, U.; Dahlin, A.M.; et al. The Genetic Architecture of Gliomagenesis–Genetic Risk Variants Linked to Specific Molecular Subtypes. Cancers 2019, 11, 2001. https://doi.org/10.3390/cancers11122001
Wu WY-Y, Johansson G, Wibom C, Brännström T, Malmström A, Henriksson R, Golovleva I, Bondy ML, Andersson U, Dahlin AM, et al. The Genetic Architecture of Gliomagenesis–Genetic Risk Variants Linked to Specific Molecular Subtypes. Cancers. 2019; 11(12):2001. https://doi.org/10.3390/cancers11122001
Chicago/Turabian StyleWu, Wendy Yi-Ying, Gunnar Johansson, Carl Wibom, Thomas Brännström, Annika Malmström, Roger Henriksson, Irina Golovleva, Melissa L. Bondy, Ulrika Andersson, Anna M. Dahlin, and et al. 2019. "The Genetic Architecture of Gliomagenesis–Genetic Risk Variants Linked to Specific Molecular Subtypes" Cancers 11, no. 12: 2001. https://doi.org/10.3390/cancers11122001
APA StyleWu, W. Y.-Y., Johansson, G., Wibom, C., Brännström, T., Malmström, A., Henriksson, R., Golovleva, I., Bondy, M. L., Andersson, U., Dahlin, A. M., & Melin, B. (2019). The Genetic Architecture of Gliomagenesis–Genetic Risk Variants Linked to Specific Molecular Subtypes. Cancers, 11(12), 2001. https://doi.org/10.3390/cancers11122001